General Stanley McChrystal holds crisis talks on his phone at a local ANA (Afghan National Army) base.

The headquarters of the International Security Assistance Force (ISAF) in Kabul looks more like a college campus than the nerve center of a military operation involving more than 90,000 troops from 41 countries, its staff officers roaming the halls in each nation's distinct patterns of camouflage. On July 3, on a wooden deck at the back of his office in the compound, shaded by trees and a garden umbrella, U.S. Army General Stanley McChrystal, who recently became ISAF's commander, and that of U.S. forces in Afghanistan, sat down to discuss his new role. Tall, lanky and earnest, with the...